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<meta name="author" content="Chen Tong" />
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Overview of IMP</a></li>
<li class="chapter" data-level="1" data-path="impchinese.html"><a href="impchinese.html"><i class="fa fa-check"></i><b>1</b> IMP中文版教程</a>
<ul>
<li class="chapter" data-level="1.1" data-path="impchinese.html"><a href="impchinese.html#impindex20"><i class="fa fa-check"></i><b>1.1</b> 首页信息</a></li>
<li class="chapter" data-level="1.2" data-path="impchinese.html"><a href="impchinese.html#impglobalsearch"><i class="fa fa-check"></i><b>1.2</b> 基于功能描述、注释或基因名字的全局搜索</a></li>
<li class="chapter" data-level="1.3" data-path="impchinese.html"><a href="impchinese.html#impsinglegene"><i class="fa fa-check"></i><b>1.3</b> 以单基因为中心的详情页面展示</a></li>
<li class="chapter" data-level="1.4" data-path="impchinese.html"><a href="impchinese.html#impgep"><i class="fa fa-check"></i><b>1.4</b> 多基因表达图谱</a></li>
<li class="chapter" data-level="1.5" data-path="impchinese.html"><a href="impchinese.html#genefishing135"><i class="fa fa-check"></i><b>1.5</b> Gene fishing 调取表达模式相近的基因</a></li>
<li class="chapter" data-level="1.6" data-path="impchinese.html"><a href="impchinese.html#gokegg"><i class="fa fa-check"></i><b>1.6</b> GO/KEGG 富集分析</a></li>
<li class="chapter" data-level="1.7" data-path="impchinese.html"><a href="impchinese.html#gsea-富集分析"><i class="fa fa-check"></i><b>1.7</b> GSEA 富集分析</a></li>
<li class="chapter" data-level="1.8" data-path="impchinese.html"><a href="impchinese.html#blastch"><i class="fa fa-check"></i><b>1.8</b> BLAST序列比对和搜索</a>
<ul>
<li class="chapter" data-level="1.8.1" data-path="impchinese.html"><a href="impchinese.html#blastnparameter"><i class="fa fa-check"></i><b>1.8.1</b> BLAST 参数参考</a></li>
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<li class="chapter" data-level="1.9" data-path="impchinese.html"><a href="impchinese.html#primerdesignch"><i class="fa fa-check"></i><b>1.9</b> 引物设计</a></li>
<li class="chapter" data-level="1.10" data-path="impchinese.html"><a href="impchinese.html#msach"><i class="fa fa-check"></i><b>1.10</b> 多序列比对展示</a></li>
<li class="chapter" data-level="1.11" data-path="impchinese.html"><a href="impchinese.html#sequencefetchch"><i class="fa fa-check"></i><b>1.11</b> 序列提取</a></li>
<li class="chapter" data-level="1.12" data-path="impchinese.html"><a href="impchinese.html#genemapviewerch"><i class="fa fa-check"></i><b>1.12</b> 基因簇可视化</a></li>
<li class="chapter" data-level="1.13" data-path="impchinese.html"><a href="impchinese.html#degeneanalysisch"><i class="fa fa-check"></i><b>1.13</b> 在线实验设计和差异基因分析</a>
<ul>
<li class="chapter" data-level="1.13.1" data-path="impchinese.html"><a href="impchinese.html#第一步实验设计确定要比较的物种和分组信息不同组织部位差异或不同处理的差异"><i class="fa fa-check"></i><b>1.13.1</b> 第一步：实验设计确定要比较的物种和分组信息（不同组织部位差异或不同处理的差异）</a></li>
<li class="chapter" data-level="1.13.2" data-path="impchinese.html"><a href="impchinese.html#第二步样品相关性评估和过滤异常样品"><i class="fa fa-check"></i><b>1.13.2</b> 第二步：样品相关性评估和过滤异常样品</a></li>
<li class="chapter" data-level="1.13.3" data-path="impchinese.html"><a href="impchinese.html#第三部设置比较组"><i class="fa fa-check"></i><b>1.13.3</b> 第三部，设置比较组</a></li>
<li class="chapter" data-level="1.13.4" data-path="impchinese.html"><a href="impchinese.html#第四步设置差异基因过滤阈值"><i class="fa fa-check"></i><b>1.13.4</b> 第四步：设置差异基因过滤阈值</a></li>
<li class="chapter" data-level="1.13.5" data-path="impchinese.html"><a href="impchinese.html#第五步概览样品信息和设置的参数这一步是提交前的信息确认"><i class="fa fa-check"></i><b>1.13.5</b> 第五步：概览样品信息和设置的参数，这一步是提交前的信息确认</a></li>
<li class="chapter" data-level="1.13.6" data-path="impchinese.html"><a href="impchinese.html#第六步差异基因分析结果报告"><i class="fa fa-check"></i><b>1.13.6</b> 第六步：差异基因分析结果报告</a></li>
</ul></li>
<li class="chapter" data-level="1.14" data-path="impchinese.html"><a href="impchinese.html#igvch"><i class="fa fa-check"></i><b>1.14</b> IGV 基因组浏览器</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="geneannotation.html"><a href="geneannotation.html"><i class="fa fa-check"></i><b>2</b> Systematic prediction and annotation of included genomes</a>
<ul>
<li class="chapter" data-level="2.1" data-path="geneannotation.html"><a href="geneannotation.html#genomeumltipleassembl"><i class="fa fa-check"></i><b>2.1</b> Species with multiple genome assembles</a></li>
<li class="chapter" data-level="2.2" data-path="geneannotation.html"><a href="geneannotation.html#genome_without_assembl"><i class="fa fa-check"></i><b>2.2</b> Species without published genome assembles</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="global_search.html"><a href="global_search.html"><i class="fa fa-check"></i><b>3</b> Global search genes by IDs, functions, and pathways</a>
<ul>
<li class="chapter" data-level="3.1" data-path="global_search.html"><a href="global_search.html#gene_detail_page"><i class="fa fa-check"></i><b>3.1</b> Gene detail page</a></li>
<li class="chapter" data-level="3.2" data-path="global_search.html"><a href="global_search.html#the-send-to-buttons"><i class="fa fa-check"></i><b>3.2</b> The send to buttons</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="browse_species_genes.html"><a href="browse_species_genes.html"><i class="fa fa-check"></i><b>4</b> Browse species and genes</a>
<ul>
<li class="chapter" data-level="4.1" data-path="browse_species_genes.html"><a href="browse_species_genes.html#structure-of-the-browse-page"><i class="fa fa-check"></i><b>4.1</b> Structure of the Browse page</a></li>
<li class="chapter" data-level="4.2" data-path="browse_species_genes.html"><a href="browse_species_genes.html#structure-of-the-species-detail-page"><i class="fa fa-check"></i><b>4.2</b> Structure of the species detail page</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="degeneanalysis.html"><a href="degeneanalysis.html"><i class="fa fa-check"></i><b>5</b> DE Gene analysis</a>
<ul>
<li class="chapter" data-level="5.1" data-path="degeneanalysis.html"><a href="degeneanalysis.html#overviewStructureform"><i class="fa fa-check"></i><b>5.1</b> Overview the structure of module page</a></li>
<li class="chapter" data-level="5.2" data-path="degeneanalysis.html"><a href="degeneanalysis.html#firststepoptionsrequiredpara"><i class="fa fa-check"></i><b>5.2</b> First step: choose options for each required parameter</a></li>
<li class="chapter" data-level="5.3" data-path="degeneanalysis.html"><a href="degeneanalysis.html#secondstepsamplecorre"><i class="fa fa-check"></i><b>5.3</b> Second step: check sample correlation profile and filter outlier samples</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="degeneanalysis.html"><a href="degeneanalysis.html#outliersampleasm"><i class="fa fa-check"></i><b>5.3.1</b> Automatical or manual detection of outlier samples</a></li>
<li class="chapter" data-level="5.3.2" data-path="degeneanalysis.html"><a href="degeneanalysis.html#interactiveheatmappca"><i class="fa fa-check"></i><b>5.3.2</b> Interactive heatmap showing sample correlation profiles</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="degeneanalysis.html"><a href="degeneanalysis.html#thirdstep"><i class="fa fa-check"></i><b>5.4</b> Third step: Set compare groups</a></li>
<li class="chapter" data-level="5.5" data-path="degeneanalysis.html"><a href="degeneanalysis.html#forthstep"><i class="fa fa-check"></i><b>5.5</b> Forth step: Set filtering thresholds for DE genes screening</a></li>
<li class="chapter" data-level="5.6" data-path="degeneanalysis.html"><a href="degeneanalysis.html#fifthstep"><i class="fa fa-check"></i><b>5.6</b> Fifth step: an overview of samples information and analysis parameter information</a></li>
<li class="chapter" data-level="5.7" data-path="degeneanalysis.html"><a href="degeneanalysis.html#degeneanalysisresultsreport"><i class="fa fa-check"></i><b>5.7</b> Sixth step: DE Gene analysis results report</a></li>
<li class="chapter" data-level="5.8" data-path="degeneanalysis.html"><a href="degeneanalysis.html#exportpdf"><i class="fa fa-check"></i><b>5.8</b> Export to PDF</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html"><i class="fa fa-check"></i><b>6</b> Gene expression profile</a>
<ul>
<li class="chapter" data-level="6.1" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#overviewStructureform2"><i class="fa fa-check"></i><b>6.1</b> Overview the structure of module page</a></li>
<li class="chapter" data-level="6.2" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#coferp13"><i class="fa fa-check"></i><b>6.2</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="6.3" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#gepdemo"><i class="fa fa-check"></i><b>6.3</b> The demo button</a></li>
<li class="chapter" data-level="6.4" data-path="geneexpressionprofile.html"><a href="geneexpressionprofile.html#precisefuzzy"><i class="fa fa-check"></i><b>6.4</b> The precise search and fuzy search mode</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="genefishing.html"><a href="genefishing.html"><i class="fa fa-check"></i><b>7</b> Gene fishing</a>
<ul>
<li class="chapter" data-level="7.1" data-path="genefishing.html"><a href="genefishing.html#genefishingcoferp5"><i class="fa fa-check"></i><b>7.1</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="7.2" data-path="genefishing.html"><a href="genefishing.html#networktoolkit"><i class="fa fa-check"></i><b>7.2</b> Network toolkit</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html"><i class="fa fa-check"></i><b>8</b> GO/KEGG enrichment analysis</a>
<ul>
<li class="chapter" data-level="8.1" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html#pgkea5"><i class="fa fa-check"></i><b>8.1</b> Principles of over-representation enrichment analysis</a></li>
<li class="chapter" data-level="8.2" data-path="GOKEGGenrichmentanalysis.html"><a href="GOKEGGenrichmentanalysis.html#coferp32"><i class="fa fa-check"></i><b>8.2</b> Choose options for each required parameters step by step</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html"><i class="fa fa-check"></i><b>9</b> GSEA enrichment analysis</a>
<ul>
<li class="chapter" data-level="9.1" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#pgsea5"><i class="fa fa-check"></i><b>9.1</b> Principles of gene set enrichment analysis (GSEA)</a></li>
<li class="chapter" data-level="9.2" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#coferp22"><i class="fa fa-check"></i><b>9.2</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="9.3" data-path="GSEAenrichmentanalysis.html"><a href="GSEAenrichmentanalysis.html#gsearef"><i class="fa fa-check"></i><b>9.3</b> References</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="genemapviewer.html"><a href="genemapviewer.html"><i class="fa fa-check"></i><b>10</b> Gene map viewer</a>
<ul>
<li class="chapter" data-level="10.1" data-path="genemapviewer.html"><a href="genemapviewer.html#coferp5"><i class="fa fa-check"></i><b>10.1</b> Choose options for each required parameters step by step</a></li>
<li class="chapter" data-level="10.2" data-path="genemapviewer.html"><a href="genemapviewer.html#oam31"><i class="fa fa-check"></i><b>10.2</b> Overlay and annotation mode</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="blast.html"><a href="blast.html"><i class="fa fa-check"></i><b>11</b> BLAST - Basic Local Alignment Search Tool</a>
<ul>
<li class="chapter" data-level="11.1" data-path="blast.html"><a href="blast.html#cusmBLAST5"><i class="fa fa-check"></i><b>11.1</b> Customizable BLAST</a></li>
<li class="chapter" data-level="11.2" data-path="blast.html"><a href="blast.html#blasthtmlresult"><i class="fa fa-check"></i><b>11.2</b> BLAST HTML results</a></li>
<li class="chapter" data-level="11.3" data-path="blast.html"><a href="blast.html#blasttableresult"><i class="fa fa-check"></i><b>11.3</b> BLAST Table results</a></li>
<li class="chapter" data-level="11.4" data-path="blast.html"><a href="blast.html#refblast"><i class="fa fa-check"></i><b>11.4</b> Reference</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="msa.html"><a href="msa.html"><i class="fa fa-check"></i><b>12</b> Multiple sequence alignment</a>
<ul>
<li class="chapter" data-level="12.1" data-path="msa.html"><a href="msa.html#sbmsa05"><i class="fa fa-check"></i><b>12.1</b> Sequences based multiple sequence alignment</a></li>
<li class="chapter" data-level="12.2" data-path="msa.html"><a href="msa.html#gtidbmsa27"><i class="fa fa-check"></i><b>12.2</b> Gene/Transcript IDs based multiple sequence alignment</a></li>
<li class="chapter" data-level="12.3" data-path="msa.html"><a href="msa.html#refmafft"><i class="fa fa-check"></i><b>12.3</b> Reference</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="sequencefetch.html"><a href="sequencefetch.html"><i class="fa fa-check"></i><b>13</b> Sequences fetch</a></li>
<li class="chapter" data-level="14" data-path="primerdesign.html"><a href="primerdesign.html"><i class="fa fa-check"></i><b>14</b> Primer design</a>
<ul>
<li class="chapter" data-level="14.1" data-path="primerdesign.html"><a href="primerdesign.html#primerdesigngeneids"><i class="fa fa-check"></i><b>14.1</b> Primer design for genes with IDs as input</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="igvbrowser.html"><a href="igvbrowser.html"><i class="fa fa-check"></i><b>15</b> IGV browser</a>
<ul>
<li class="chapter" data-level="15.1" data-path="igvbrowser.html"><a href="igvbrowser.html#vepigv"><i class="fa fa-check"></i><b>15.1</b> Visualizing expression profiles</a></li>
</ul></li>
<li class="chapter" data-level="16" data-path="download.html"><a href="download.html"><i class="fa fa-check"></i><b>16</b> Download</a></li>
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<div id="degeneanalysis" class="section level1 hasAnchor" number="5">
<h1><span class="header-section-number">5</span> DE Gene analysis<a href="degeneanalysis.html#degeneanalysis" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Using <a href="https://bioconductor.org/packages/release/bioc/html/limma.html"><code>limma-voom</code></a> to screen DE genes based on Read-count expression data and performing GO/KEGG enrichment analysis for differentially Expressed (DE) genes.</p>
<div id="overviewStructureform" class="section level2 hasAnchor" number="5.1">
<h2><span class="header-section-number">5.1</span> Overview the structure of module page<a href="degeneanalysis.html#overviewStructureform" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Every functional module has the same structures including one or several forms for parameter customization. Some common explanations for these forms are listed below:</p>
<ol style="list-style-type: decimal">
<li>Module descriptions are listed above.</li>
<li>A demo button is supplied for quick filling in all required parameters. One just needs to click the <code>Submit</code> button to get the results or move to the next steps.</li>
<li>Each parameter has an <code>i</code> symbol to show the explanations of related parameters.</li>
<li>Not all parameters are required.</li>
</ol>
<blockquote>
<p>Note</p>
<ol style="list-style-type: decimal">
<li>Parameters with a red star (<font color='#FF0000'>*</font>) before are mandatory parameters.</li>
<li>Parameters without a red star (<font color='#FF0000'>*</font>) before are optional parameters. For optional parameters, if left unselected, all options are default selected.</li>
</ol>
</blockquote>
<ol start="5" style="list-style-type: decimal">
<li>In the case of the chosen of un-existed parameter combinations, drop-down values of each parameter depend on the selection of its upstream parameters. And also, changing the selection of one parameter would clear up any selected values of downstream parameters.</li>
</ol>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-50"></span>
<img src="image/form_overview.png" alt="A screenshot of the form structure." width="100%" />
<p class="caption">
Figure 5.1: A screenshot of the form structure.
</p>
</div>
</div>
<div id="firststepoptionsrequiredpara" class="section level2 hasAnchor" number="5.2">
<h2><span class="header-section-number">5.2</span> First step: choose options for each required parameter<a href="degeneanalysis.html#firststepoptionsrequiredpara" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Just select each parameter sequentially as labeled in the figure.</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-51"></span>
<img src="image/de_gene_analysis_first_step.png" alt="A screenshot of the first step of DE gene analysis." width="100%" />
<p class="caption">
Figure 5.2: A screenshot of the first step of DE gene analysis.
</p>
</div>
</div>
<div id="secondstepsamplecorre" class="section level2 hasAnchor" number="5.3">
<h2><span class="header-section-number">5.3</span> Second step: check sample correlation profile and filter outlier samples<a href="degeneanalysis.html#secondstepsamplecorre" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>When samples are selected, the module first integrates the raw expression value of all samples to form the read-count matrix. Then the size factor is estimated like in the R package <a href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html">DESeq2</a> to generate a normalized expression matrix.</p>
<div id="outliersampleasm" class="section level3 hasAnchor" number="5.3.1">
<h3><span class="header-section-number">5.3.1</span> Automatical or manual detection of outlier samples<a href="degeneanalysis.html#outliersampleasm" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Samples passed the outlier sample detection are defined as normal samples. All samples in the <code>Sample passed filter</code> box would be treated as normal samples (corresponding to outlier samples) and will be used for downstream analysis. The checkboxes were used for sample transfer only.</p>
<blockquote>
<p>Definition of outlier samples</p>
<p>Outlier samples were defined as those that have abnormal low overall similarity with all other samples. For one sample A, the overall similarity with all other samples is defined as K which equals the sum of the person correlation value of A with all other samples. Then the K for all samples was scale-transformed. The ones with scale-transformed K less than -4 were defined as outlier samples.</p>
</blockquote>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-52"></span>
<img src="image/sample_compare_transfer_box.png" alt="A screenshot of outlier sample detection." width="100%" />
<p class="caption">
Figure 5.3: A screenshot of outlier sample detection.
</p>
</div>
<p>Also, users are allowed to select any sample as an outlier sample based on the sample correlation heatmap and PCA plots below and manually transfer these samples to the <code>Pontential outlier samples</code> box.</p>
<blockquote>
<p>Outlier sample detection principle</p>
</blockquote>
<blockquote>
<p>Abnormal samples were detected using Z-score Method. A Z-score (or standard score) represents how many standard deviations a given measurement deviates from the mean. Here the measurement represents the correlation between one sample to all other samples. In other words, Z-score merely re-scales, or standardizes your data. A Z-score serves to specify the precise location of each observation within a distribution. The sign of the Z-score (+ or -) indicates whether the score is above (+) or below (-) the mean.</p>
</blockquote>
<blockquote>
<p>Z-score with value 3 is a common cut-off in practice for identifying outliers in a Gaussian or Gaussian-like distribution. For smaller samples of data, perhaps a value of 2 can be used, and for larger samples, perhaps a value of 4 can be used.</p>
</blockquote>
</div>
<div id="interactiveheatmappca" class="section level3 hasAnchor" number="5.3.2">
<h3><span class="header-section-number">5.3.2</span> Interactive heatmap showing sample correlation profiles<a href="degeneanalysis.html#interactiveheatmappca" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>The sample correlation heatmap and PCA analysis were performed and the results listed below.</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-53"></span>
<img src="image/sample_compare_heatmap.png" alt="Heatmap showing expression profile of 12 samples. DE_Group: Biological groups detected based on metadata and user selection. Single_group: check if one biological group only contains one sample. Single_batch: check if one specified batch only contains one sample. Outlier: Potential outlier samples when this value is true. Suggest_remove: Samples with this value as true would be automatically removed." width="100%" />
<p class="caption">
Figure 5.4: Heatmap showing expression profile of 12 samples. <code>DE_Group</code>: Biological groups detected based on metadata and user selection. <code>Single_group</code>: check if one biological group only contains one sample. <code>Single_batch</code>: check if one specified batch only contains one sample. <code>Outlier</code>: Potential outlier samples when this value is <code>true</code>. <code>Suggest_remove</code>: Samples with this value as <code>true</code> would be automatically removed.
</p>
</div>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-54"></span>
<img src="image/sample_compare_pca.png" alt="The principle component analysis (PCA) shows sample distributions in PC1 and PC2 space. In the Toolkit part, users could select to change PC1-PC2 space to other principle components constructed space. Also, point color, point shape, and point size could be mapped by different sample attributes for data exploration. X/Y marginal plot could generate sample distribution along PCxx axis." width="100%" />
<p class="caption">
Figure 5.5: The principle component analysis (PCA) shows sample distributions in PC1 and PC2 space. In the <code>Toolkit</code> part, users could select to change PC1-PC2 space to other principle components constructed space. Also, point color, point shape, and point size could be mapped by different sample attributes for data exploration. <code>X/Y marginal plot</code> could generate sample distribution along PCxx axis.
</p>
</div>
<blockquote>
<p>Note</p>
<p>Some plots have a <code>Toolkit</code> button at its right-topp corner.</p>
<ol style="list-style-type: decimal">
<li><code>Export SVG</code> could export the plot in SVG format for further processing on the local computer.</li>
<li>Other parameters to change picture attributes or picture contents.</li>
</ol>
</blockquote>
</div>
</div>
<div id="thirdstep" class="section level2 hasAnchor" number="5.4">
<h2><span class="header-section-number">5.4</span> Third step: Set compare groups<a href="degeneanalysis.html#thirdstep" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>For this example, we want to check the expression differences along inducing. We may first compare each induced stage (<code>MeJA_12_hours</code>, <code>MeJA_24_hours</code>, and <code>MeJA_48_hours</code>) with the initial stage (<code>MeJA_0_hours</code>).</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-55"></span>
<img src="image/drag_sample_group.png" alt="Set compare groups." width="100%" />
<p class="caption">
Figure 5.6: Set compare groups.
</p>
</div>
<blockquote>
<p>Note</p>
<p>Simple and complex comparation relationships could be constructed.</p>
<ol style="list-style-type: decimal">
<li><code>icMERS_treat_12h-icMERS_mock_12h</code>: compare between treat and mock samples at 12 hours.</li>
<li><code>(icMERS_treat_12h-icMERS_mock_12h)-(icMERS_treat_0h-icMERS_mock_0h)</code>: compare the effect of icMERS treat for 12 h after removing the difference of each mock sample.</li>
</ol>
</blockquote>
</div>
<div id="forthstep" class="section level2 hasAnchor" number="5.5">
<h2><span class="header-section-number">5.5</span> Forth step: Set filtering thresholds for DE genes screening<a href="degeneanalysis.html#forthstep" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Genes with detected FDR values less than the user-specified values and absolute log2 transformed expression fold change no less than the given value would be treated as DE genes.</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-56"></span>
<img src="image/sample_compare_de_ananlysis_parameter.png" alt="Set the FDR and absolute Log2FC for screening DE genes." width="100%" />
<p class="caption">
Figure 5.7: Set the FDR and absolute Log2FC for screening DE genes.
</p>
</div>
</div>
<div id="fifthstep" class="section level2 hasAnchor" number="5.6">
<h2><span class="header-section-number">5.6</span> Fifth step: an overview of samples information and analysis parameter information<a href="degeneanalysis.html#fifthstep" class="anchor-section" aria-label="Anchor link to header"></a></h2>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-57"></span>
<img src="image/DE_gene_analysis_overview_samples_parameters.png" alt="Overview of the sample information and parameter information." width="100%" />
<p class="caption">
Figure 5.8: Overview of the sample information and parameter information.
</p>
</div>
<blockquote>
<p>Note</p>
<p>An email address is optional but not required for receiving the results. After clicking ‘Start analysis’, the web page would be re-directed to the result page, in which the result link would be put into the web pocket for later access. If the email address is given, the result link would also be sent to a given address.</p>
</blockquote>
</div>
<div id="degeneanalysisresultsreport" class="section level2 hasAnchor" number="5.7">
<h2><span class="header-section-number">5.7</span> Sixth step: DE Gene analysis results report<a href="degeneanalysis.html#degeneanalysisresultsreport" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>A report including sample information, sample correlation visualization, DE genes heatmap, and volcano plot, Functional enrichment results would be shown on the result page.</p>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-58"></span>
<img src="image/sample_compare_result_navigation.png" alt="Table of content showing the structure of the report and navigating to each resulting part." width="100%" />
<p class="caption">
Figure 5.9: Table of content showing the structure of the report and navigating to each resulting part.
</p>
</div>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-59"></span>
<img src="image/de_gene_result_page1.png" alt="The first part of the DE gene result report includes whole sample information, and sample correlation information." width="100%" />
<p class="caption">
Figure 5.10: The first part of the DE gene result report includes whole sample information, and sample correlation information.
</p>
</div>

<div class="figure" style="text-align: center"><span style="display:block;" id="fig:unnamed-chunk-60"></span>
<img src="image/de_gene_result_page2.png" alt="The second part of the DE gene result report includes DE gene heatmap, volcano plot, and functional enrichment result." width="100%" />
<p class="caption">
Figure 5.11: The second part of the DE gene result report includes DE gene heatmap, volcano plot, and functional enrichment result.
</p>
</div>
</div>
<div id="exportpdf" class="section level2 hasAnchor" number="5.8">
<h2><span class="header-section-number">5.8</span> Export to PDF<a href="degeneanalysis.html#exportpdf" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>When all the results are loading, pressing <code>Ctrl + p</code> would start the <code>Printer to PDF</code> function to output the result to a PDF version report.</p>

</div>
</div>
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